Hi Charlie,
In the alignment file have you tried sth like the construct below?
>P1;template <SNIP> YIK/.*
>P1;target <SNIP> HIK/.*
Make sure your residue selection includes your NAD ie structureX:template:1:A:4:A:.:.:.:. for the example given would correspond to the pdb file template.pdb with TYR 1 A, ... FAD 4 A
Cheers, Ralf
============================================ Dr Ralf Schmid Lecturer in Bioinformatics Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road Leicester LE1 9HN UK
Tel. +44 (0)116 229 7023 ============================================
> -----Original Message----- > From: modeller_usage-bounces@salilab.org > [mailto:modeller_usage-bounces@salilab.org] On Behalf Of > Charlie Allerston > Sent: 15 March 2007 16:22 > To: modeller-care@salilab.org > Cc: modeller_usage@salilab.org > Subject: Re: [modeller_usage] How to incorporate NAD and > water in my model > > > >Charlie Allerston wrote: > >>Do you have to use the modeller alignment script? I have > been using > >>ebi software to create a .pir file. > > > >No, you do not need to use Modeller to make your alignment file. > >However, since there are no standard one-letter codes for > ligands, you > >will likely have to edit your original alignment in a text editor to > >put in the ligands. > > > > This is what I am not getting. Where to put the ligand in > the alignment, regardless of what character to use. > Take this for instance. trying to model something from the > template 1VDC http://www.rcsb.org/pdb/explore.do?structureId=1VDC > Looking at the PDB file it has 316 residues then it had a > molecule of FAD tacked on at a position designated 400. > So when I align this to some target like below (cropped). > > > --------------------------MNGLETHNTRLCIVGSGPAAHTAAIYAARAELKP > LLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTK > VDFSSKPFKLFTDS---KAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCD > GAAPIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKID > VIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELD > SDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQEIGSQEGK > SD- > * > >P1;fake1 > > DASGLSVAAAATLSQKSTPYYQSEIHTIGKRRMHSKVVIIGSGPAAHTAAIYLARAELKP > VLYEGFMANGVAAGGQLTTTTEVENFPGFPEAVTGQELMDKMRAQSERFGTVIVSETVGK > LDLSKRPFEYSTEWSPDTVMTADAVILATGASARRLGLPGED----KYWQNGISACAVCD > GAVPIFRNKPLVVIGGGDSAAEEAIFLTKYGSHVTVLVRRDKLRASSIMARRLLAN---- > ------------------------------------------------------------ > -------------KKVTGLFAAGDVQDKRYRQAITSAGTGCMAALDAEKYLEELEDEQAD > GKL > * > > Where should I stick the fad? At the end? How many blk > characters should I tack on? 1 because there is only one > molecule? Is there a specific character for FAD? > > These are my stumbling blocks. > > regards > > _________________________________________________________________ > Solve the Conspiracy and win fantastic prizes. > http://www.theconspiracygame.co.uk/ > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >